Predicting stochastic gene expression dynamics in single cells

Jerome T. Mettetal, Dale Muzzey, Juan M. Pedraza, Ertugrul M. Ozbudak, Alexander Van Oudenaarden

Research output: Contribution to journalArticle

121 Citations (Scopus)

Abstract

Fluctuations in protein numbers (noise) due to inherent stochastic effects in single cells can have large effects on the dynamic behavior of gene regulatory networks. Although deterministic models can predict the average network behavior, they fail to incorporate the stochasticity characteristic of gene expression, thereby limiting their relevance when single cell behaviors deviate from the population average. Recently, stochastic models have been used to predict distributions of steady-state protein levels within a population but not to predict the dynamic, presteady-state distributions. In the present work, we experimentally examine a system whose dynamics are heavily influenced by stochastic effects. We measure population distributions of protein numbers as a function of time in the Escherichia coli lactose uptake network (lac operon). We then introduce a dynamic stochastic model and show that prediction of dynamic distributions requires only a few noise parameters in addition to the rates that characterize a deterministic model. Whereas the deterministic model cannot fully capture the observed behavior, our stochastic model correctly predicts the experimental dynamics without any fit parameters. Our results provide a proof of principle for the possibility of faithfully predicting dynamic population distributions from deterministic models supplemented by a stochastic component that captures the major noise sources.

Original languageEnglish (US)
Pages (from-to)7304-7309
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume103
Issue number19
DOIs
StatePublished - May 9 2006
Externally publishedYes

Fingerprint

Noise
Gene Expression
Demography
Proteins
Lac Operon
Gene Regulatory Networks
Lactose
Population
Escherichia coli

Keywords

  • Gene networks
  • Systems biology

ASJC Scopus subject areas

  • Genetics
  • General

Cite this

Predicting stochastic gene expression dynamics in single cells. / Mettetal, Jerome T.; Muzzey, Dale; Pedraza, Juan M.; Ozbudak, Ertugrul M.; Van Oudenaarden, Alexander.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 19, 09.05.2006, p. 7304-7309.

Research output: Contribution to journalArticle

Mettetal, Jerome T. ; Muzzey, Dale ; Pedraza, Juan M. ; Ozbudak, Ertugrul M. ; Van Oudenaarden, Alexander. / Predicting stochastic gene expression dynamics in single cells. In: Proceedings of the National Academy of Sciences of the United States of America. 2006 ; Vol. 103, No. 19. pp. 7304-7309.
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